Abstract：
Accurate species-level identification of Enterobacter cloacae complex (ECC) is crucial for related research. The classification of ECC is based on strain-to-strain phylogenetic congruence, as well as genomic features including average nucleotide identity (ANI) and digitalized DNA-DNA hybridization (dDDH). ANI and dDDH derived from whole-genome sequencing have emerged as a reliable metric for assessing genetic relatedness between genomes and are increasingly recognized as a standard for species delimitation. Up to now, there are two different classification methods for ECC. The first one categorizes E. hormaechei, a species within ECC, into five subspecies (E. hormaechei subsp. steigerwaltii, subsp. oharae, subsp. xiangfangensis, subsp. hoffmannii, and subsp. hormaechei). The second classifies E. hormaechei as three species: E. hormaechei, \"E. xiangfangensis,\" \"E. hoffmanii.\" While the former is well-accepted in the academic area, the latter may have a greater ability to distinguish different species of ECC. To assess the suitability of these identification criteria for clinical ECC isolates, we conducted a comprehensive analysis involving phylogenetic analysis, ANI and dDDH value alignment, virulence gene identification, and capsule typing on 256 clinical ECC strains isolated from the bloodstream. Our findings indicated that the method of categorizing E. hormaechei into five subspecies has better correlation and consistency with the molecular characteristics of clinical ECC isolates, as evidenced by phylogenetic analysis, virulence genes, and capsule typing. Therefore, the subspecies-based classification method appears more suitable for taxonomic assignments of clinical ECC isolates.
OBJECTIVE: Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.
OBJECTIVE: Standardizing taxonomy of the Enterobacter cloacae complex (ECC) is necessary for data integration across diverse studies. The study utilized whole-genome data to accurately identify 256 clinical ECC isolated from bloodstream infections using average nucleotide identity (ANI), digitalized DNA-DNA hybridization (dDDH), and phylogenetic analysis. Through comprehensive assessments including phylogenetic analysis, ANI and dDDH comparisons, virulence gene, and capsule typing of the 256 clinical isolates, it was concluded that the classification method based on subspecies exhibited better correlation and consistency with the molecular characteristics of clinical ECC isolates. In summary, this research contributes to the precise identification of clinical ECC at the species level and expands our understanding of ECC.
摘要：
阴沟肠杆菌复合体(ECC)的准确种级鉴定对相关研究至关重要。ECC的分类是基于菌株到菌株的系统发育一致性，以及基因组特征，包括平均核苷酸同一性（ANI）和数字化DNA-DNA杂交（dDDH）。来自全基因组测序的ANI和dDDH已成为评估基因组之间遗传相关性的可靠指标，并且越来越被认为是物种定界的标准。到目前为止,ECC有两种不同的分类方法。第一个分类是E.hormaechei，ECC中的一个物种，分为五个亚种(E.hormaechei亚科。steigerwaltii,subsp.oharae,subsp.香房,subsp.霍夫曼尼,和subsp。hormaechei）。第二个将E.hormaechei分类为三个物种：E.hormaechei，\"E.香房,\"\"E.Hoffmanii.“虽然前者在学术领域被广泛接受，后者可能具有更大的区分不同种类的ECC的能力。为了评估这些鉴定标准对临床ECC分离株的适用性，我们进行了包括系统发育分析的全面分析，ANI和dDDH值对齐，毒力基因鉴定，并对从血液中分离出的256种临床ECC菌株进行胶囊分型。我们的发现表明，将Hormaechei大肠杆菌分类为五个亚种的方法与临床ECC分离株的分子特征具有更好的相关性和一致性。正如系统发育分析所证明的那样，毒力基因，和胶囊打字。因此,基于亚种的分类方法似乎更适合于临床ECC分离株的分类分配.
目的：阴沟肠杆菌复合体（ECC）的标准化分类对于跨不同研究的数据整合是必要的。该研究利用全基因组数据，使用平均核苷酸同一性（ANI）准确鉴定了从血流感染中分离出的256种临床ECC。数字化DNA-DNA杂交（dDDH），和系统发育分析。通过包括系统发育分析在内的全面评估，ANI和dDDH比较，毒力基因，和256个临床分离株的胶囊分型，结论是，基于亚种的分类方法与临床ECC分离株的分子特征具有更好的相关性和一致性。总之,这项研究有助于在物种水平上精确识别临床ECC,并扩展了我们对ECC的理解.
目的：阴沟肠杆菌复合体（ECC）的标准化分类对于跨不同研究的数据整合是必要的。该研究利用全基因组数据，使用平均核苷酸同一性（ANI）准确鉴定了从血流感染中分离出的256种临床ECC。数字化DNA-DNA杂交（dDDH），和系统发育分析。通过包括系统发育分析在内的全面评估，ANI和dDDH比较，毒力基因，和256个临床分离株的胶囊分型，结论是，基于亚种的分类方法与临床ECC分离株的分子特征具有更好的相关性和一致性。总之,这项研究有助于在物种水平上精确识别临床ECC,并扩展了我们对ECC的理解.
